I would flush the A/C system prior to removing the hoses as it's easier and less messy to access and catch the solvent.
The single biggest mistake many make with an A/C upgrade is to install the R134a pump with it's PAG oil on an R12 system with mineral oil. The two are not compatible and will gum up the system. We drain new compressors overnight flush the system and use Ester oil which is compatible with both.
The second biggest mistake is not changing the evaporator valve under the dash. The R134a requires a smaller orifice to achieve the desired pressure drop across the valve. this it typically why folks blow high pressure hoses first.
Julian
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